chr16-53522178-C-T

Variant names:

• chr16-53522178-C-T
• rs11863156

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.436 in 151,892 control chromosomes in the GnomAD database, including 15,938 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15938 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66190 AN: 151774 Hom.: 15893 Cov.: 30

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.428

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.436 AC: 66300 AN: 151892 Hom.: 15938 Cov.: 30 AF XY: 0.433 AC XY: 32142 AN XY: 74244

African (AFR) AF: 0.636 AC: 26294 AN: 41364

American (AMR) AF: 0.449 AC: 6839 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2592 AN: 5162

South Asian (SAS) AF: 0.451 AC: 2176 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2691 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23060 AN: 67948

Other (OTH) AF: 0.436 AC: 920 AN: 2112

Alfa AF: 0.400 Hom.: 5644

Bravo AF: 0.459

Asia WGS AF: 0.519 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		-0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11863156; hg19: chr16-53556090;